Clazz.declarePackage("JS");
Clazz.load(["JS.ScriptParam"], "JS.ScriptExpr", ["java.util.Hashtable", "JU.BS", "$.CU", "$.Lst", "$.Measure", "$.P3", "$.PT", "$.SB", "J.api.Interface", "JM.AtomCollection", "$.BondSet", "$.Group", "$.ModelSet", "JS.SV", "$.ScriptMathProcessor", "$.T", "JU.BSUtil", "$.Edge", "$.Elements", "$.Escape"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.debugHigh = false;
this.privateFuncs = null;
this.cmdExt = null;
this.isoExt = null;
this.mathExt = null;
this.smilesExt = null;
this.tempStatement = null;
this.ptTemp = null;
Clazz.instantialize(this, arguments);}, JS, "ScriptExpr", JS.ScriptParam);
Clazz.defineMethod(c$, "getCmdExt", 
function(){
return (this.cmdExt == null ? this.cmdExt = (this.getExt("Cmd")).init(this) : this.cmdExt);
});
Clazz.defineMethod(c$, "getIsoExt", 
function(){
return (this.isoExt == null ? this.isoExt = (this.getExt("Iso")).init(this) : this.isoExt);
});
Clazz.defineMethod(c$, "getMathExt", 
function(){
return (this.mathExt == null ? (this.mathExt = this.getExt("Math")).init(this) : this.mathExt);
});
Clazz.defineMethod(c$, "getSmilesExt", 
function(){
return (this.smilesExt == null ? (this.smilesExt = this.getExt("Smiles")).init(this) : this.smilesExt);
});
Clazz.defineMethod(c$, "getExt", 
function(type){
return J.api.Interface.getInterface("JS." + type + "Ext", this.vwr, "script");
}, "~S");
Clazz.defineMethod(c$, "parameterExpressionList", 
function(pt, ptAtom, isArrayItem){
return this.parameterExpression(pt, -1, null, true, true, ptAtom, isArrayItem, null, null, false);
}, "~N,~N,~B");
Clazz.defineMethod(c$, "parameterExpressionString", 
function(pt, ptMax){
return this.parameterExpression(pt, ptMax, "", true, false, -1, false, null, null, false);
}, "~N,~N");
Clazz.defineMethod(c$, "parameterExpressionBoolean", 
function(pt, ptMax){
return (this.parameterExpression(pt, ptMax, null, true, false, -1, false, null, null, false)).booleanValue();
}, "~N,~N");
Clazz.defineMethod(c$, "parameterExpressionToken", 
function(pt){
var result = this.parameterExpressionList(pt, -1, false);
return (result.size() > 0 ? result.get(0) : JS.SV.newS(""));
}, "~N");
Clazz.defineMethod(c$, "parameterExpressionSelect", 
function(h, where){
this.st = where;
this.slen = this.st.length;
return (this.parameterExpression(2, -2147483648, null, true, false, -1, false, h, null, false)).booleanValue();
}, "java.util.Map,~A");
Clazz.defineMethod(c$, "parameterExpression", 
function(pt, ptMax, key, ignoreComma, asVector, ptAtom, isArrayItem, localVars, localVar, isSpecialAssignment){
var isImplicitAtomProperty = (localVar != null);
var isWhere = (localVar == null && localVars != null);
var isOneExpressionOnly = (pt < 0);
var returnBoolean = (!asVector && key == null);
var returnString = (!asVector && key != null && key.length == 0);
if (isOneExpressionOnly) pt = -pt;
var allContext = (localVars == null || ptMax != -2147483648);
if (ptMax < pt) ptMax = this.slen;
var ptEq = (isSpecialAssignment ? 0 : 1);
var ptWithin = -1;
var rpn =  new JS.ScriptMathProcessor(this, isSpecialAssignment, isArrayItem, asVector, false, false, key);
var v;
var res;
var nSquare = 0;
var nParen = 0;
var topLevel = true;
out : for (var i = pt; i < ptMax; i++) {
v = null;
var tok = this.getToken(i).tok;
if (isImplicitAtomProperty && this.tokAt(i + 1) != 1073742336) {
var token = (localVars != null && localVars.containsKey(this.theToken.value) ? null : this.getBitsetPropertySelector(i, 10));
if (token != null) {
rpn.addX(localVars.get(localVar));
if (!rpn.addOpAllowMath(token, (this.tokAt(i + 1) == 268435968), 0)) this.invArg();
if ((token.intValue == 134320141 || token.intValue == 102436) && this.tokAt(this.iToken + 1) != 268435968) {
rpn.addOp(JS.T.tokenLeftParen);
rpn.addOp(JS.T.tokenRightParen);
}i = this.iToken;
continue;
}}switch (tok) {
case 268437505:
case 1073742338:
if (!ignoreComma && topLevel) break out;
if (tok == 1073742338) this.invArg();
if (isSpecialAssignment && nSquare == 1 && this.tokAt(i + 1) == 268440324) isSpecialAssignment = rpn.endAssignment();
}
switch (tok) {
case 12290:
if ((tok = this.tokAt(++i)) == 1073742325) {
v = this.parameterExpressionToken(++i);
i = this.iToken;
} else if (tok == 2) {
v = this.vwr.ms.getAtoms(1094715393, Integer.$valueOf(this.st[i].intValue));
break;
} else if (tok == 12290 && this.tokAt(i + 1) == 2) {
v = this.vwr.ms.getAtomsFromAtomNumberInFrame(this.st[++i].intValue);
break;
} else {
v = this.getParameter(JS.SV.sValue(this.st[i]), 1073742190, true);
}v = this.getParameter((v).asString(), 1073742190, true);
break;
case 134320649:
if (this.getToken(++i).tok != 268435968) this.invArg();
if (localVars == null) localVars =  new java.util.Hashtable();
res = this.parameterExpression(++i, -1, null, ignoreComma, false, -1, false, localVars, localVar, false);
var TF = (res).booleanValue();
var iT = this.iToken;
if (this.getToken(iT++).tok != 1073742339) this.invArg();
this.parameterExpressionBoolean(iT, -1);
var iF = this.iToken;
if (this.tokAt(iF++) != 1073742339) this.invArg();
this.parameterExpression(-iF, -1, null, ignoreComma, false, 1, false, localVars, localVar, false);
var iEnd = this.iToken;
if (this.tokAt(iEnd) != 268435969) this.invArg();
v = this.parameterExpression(TF ? iT : iF, TF ? iF : iEnd, "XXX", ignoreComma, false, 1, false, localVars, localVar, false);
i = this.iToken = iEnd;
break;
case 134320648:
case 1275082241:
var isFunctionOfX = (pt > 0);
var isFor = (isFunctionOfX && tok == 134320648);
var dummy;
if (isFunctionOfX) {
if (this.getToken(++i).tok != 268435968 || !JS.T.tokAttr(this.getToken(++i).tok, 1073741824)) this.invArg();
dummy = this.paramAsStr(i);
if (this.getToken(++i).tok != 1073742339) this.invArg();
} else {
dummy = "_x";
}v = this.parameterExpressionToken(-(++i)).value;
if (!(Clazz.instanceOf(v,"JU.BS"))) this.invArg();
var bsAtoms = v;
i = this.iToken;
if (isFunctionOfX && this.getToken(i++).tok != 1073742339) this.invArg();
var bsSelect =  new JU.BS();
var bsX =  new JU.BS();
var sout = (isFor ?  new Array(bsAtoms.cardinality()) : null);
if (localVars == null) localVars =  new java.util.Hashtable();
bsX.set(0);
var t = JS.SV.newV(10, bsX);
t.index = 0;
localVars.put(dummy, t.setName(dummy));
var pt2 = -1;
if (isFunctionOfX) {
pt2 = i - 1;
var np = 0;
var tok2;
while (np >= 0 && ++pt2 < ptMax) {
if ((tok2 = this.tokAt(pt2)) == 268435969) np--;
 else if (tok2 == 268435968) np++;
}
}var p = 0;
var jlast = 0;
var j = bsAtoms.nextSetBit(0);
if (j < 0 || this.chk) {
this.iToken = pt2 - 1;
} else {
for (; j >= 0; j = bsAtoms.nextSetBit(j + 1)) {
if (jlast >= 0) bsX.clear(jlast);
jlast = j;
bsX.set(j);
t.index = j;
res = this.parameterExpression(i, pt2, (isFor ? "XXX" : null), ignoreComma, isFor, j, false, localVars, isFunctionOfX ? null : dummy, false);
if (isFor) {
if (res == null || (res).size() == 0) this.invArg();
sout[p++] = ((res).get(0)).asString();
} else if ((res).booleanValue()) {
bsSelect.set(j);
}}
}if (isFor) {
v = sout;
} else if (isFunctionOfX) {
v = bsSelect;
} else {
return this.listBS(bsSelect);
}i = this.iToken + 1;
break;
case 1073742339:
break out;
case 2:
if (this.tokAt(this.iToken + 1) == 1073742336 && ((tok = this.tokAt(this.iToken + 2)) == 805307393 || tok == 268441089)) {
this.theToken.value = Float.$valueOf(this.theToken.intValue);
this.theToken.tok = 3;
this.theToken.intValue = 2147483647;
i++;
}case 3:
case 1073742362:
rpn.addXNum(this.theToken);
break;
case 134217750:
if (this.tokAt(this.iToken + 1) == 268435968) {
if (!rpn.addOpAllowMath(this.theToken, true, 0)) this.invArg();
break;
}case 1073742335:
case 1073742334:
case 4:
case 8:
case 9:
case 11:
case 12:
case 7:
case 10:
case 6:
case 14:
rpn.addX(JS.SV.newT(this.theToken));
break;
case 1073742330:
if (this.tokAt(i + 2) == 1073742336 && this.tokAt(i + 3) == 1275072526) {
rpn.addXStr("$" + this.paramAsStr(++i));
} else {
this.ignoreError = true;
var ptc;
try {
ptc = this.centerParameter(i, null);
rpn.addX(JS.SV.newV(8, ptc));
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
rpn.addXStr("");
} else {
throw e;
}
}
this.ignoreError = false;
i = this.iToken;
}break;
case 1073742332:
if (this.tokAt(i + 1) == 4) {
if (this.tokAt(i + 2) == 1073742338) {
v = (this.chk ?  new JU.BS() : this.getAtomBitSet(this.stringParameter(i + 1)));
i += 2;
break;
}v = this.getAssocArray(i);
} else {
v = this.getPointOrPlane(i, 55);
}i = this.iToken;
break;
case 1073742340:
v = this.vwr.getFrameAtoms();
i = this.iToken;
break;
case 1073742325:
if (this.tokAt(i + 1) == 1073742326) {
v =  new java.util.Hashtable();
i++;
break;
} else if (this.tokAt(i + 1) == 1073742327 && this.tokAt(i + 2) == 1073742326) {
tok = 1073742327;
this.iToken += 2;
}case 1073742327:
if (tok == 1073742327) v = this.vwr.getAllAtoms();
 else v = this.atomExpression(this.st, i, 0, true, true, null, true);
i = this.iToken;
if (nParen == 0 && isOneExpressionOnly) {
this.iToken++;
return this.listBS(v);
}break;
case 1073742195:
rpn.addOp(this.theToken);
continue;
case 1073742326:
i++;
break out;
case 268436992:
if (!ignoreComma && topLevel) break out;
if (!rpn.addOp(this.theToken)) this.invArg();
break;
case 1073742337:
case 1073742336:
if (isSpecialAssignment && topLevel && this.tokAt(i + 2) == 268440324) isSpecialAssignment = rpn.endAssignment();
if (ptEq == 0 && topLevel) {
switch (this.tokAt(i + 1)) {
case 0:
break;
case 1275335685:
case 1275334681:
case 1140850694:
case 1140850706:
case 1140850696:
case 1275068418:
if (tok == 1073742336) break;
default:
rpn.addOp(JS.T.tokenArrayOpen);
rpn.addXStr(this.optParameterAsString(++i));
rpn.addOp(JS.T.tokenArrayClose);
continue;
}
}var $var = this.getBitsetPropertySelector(i + 1, rpn.getXTok());
var tok1 = $var.intValue;
var isUserFunction = (tok1 == 134320141);
var allowMathFunc = true;
var tok2 = this.tokAt(this.iToken + 2);
if (this.tokAt(this.iToken + 1) == 1073742336) {
switch (tok2) {
case 1073742327:
tok2 = 480;
if (this.tokAt(this.iToken + 3) == 1073742336 && this.tokAt(this.iToken + 4) == 1275068420) tok2 = 224;
case 1275068725:
case 32:
case 64:
case 192:
case 128:
case 160:
case 96:
allowMathFunc = (isUserFunction || tok1 == 1275069443 || tok2 == 480 || tok2 == 224 || tok2 == 1275068725);
$var.intValue |= tok2 & 480;
this.getToken(this.iToken + 2);
if (this.tokAt(this.iToken + 1) == 268435968 && tok1 != 1275069443) {
this.iToken += 2;
}}
}var tokNext = this.tokAt(this.iToken + 1);
allowMathFunc = new Boolean (allowMathFunc & (tokNext == 268435968 || isUserFunction)).valueOf();
if (!rpn.addOpAllowMath($var, allowMathFunc, isUserFunction ? tokNext : 0)) this.invArg();
i = this.iToken;
if ($var.intValue == 134320141 && tokNext != 268435968) {
rpn.addOp(JS.T.tokenLeftParen);
rpn.addOp(JS.T.tokenRightParen);
}break;
case 1153433601:
case 1086326786:
case 1086326785:
case 1073742328:
case 1812599299:
case 1086326788:
case 1073742329:
case 1111490587:
case 1086326789:
case 1086324742:
case 1094717454:
case 1094713360:
case 1073742128:
case 134218756:
case 1086324744:
case 1094713366:
case 134218757:
case 1237320707:
case 1639976963:
if (!isWhere && i == ptWithin && this.tokAt(i + 1) == 268436992) {
rpn.addX(JS.SV.newT(this.theToken));
break;
}default:
if (this.theTok == 268437504 && this.tokAt(i + 2) == 268436482) {
v = this.getAssocArray(i);
i = this.iToken;
break;
}if (JS.T.tokAttr(this.theTok, 268435456) || JS.T.tokAttr(this.theTok, 134217728) && this.tokAt(this.iToken + 1) == 268435968) {
if (!rpn.addOp(this.theToken)) {
if (ptAtom >= 0) {
break out;
}this.invArg();
}switch (this.theTok) {
case 134217759:
ptWithin = i + 2;
break;
case 268440324:
if (topLevel) ptEq = i;
break;
case 268435968:
nParen++;
topLevel = false;
break;
case 268435969:
if (--nParen <= 0 && nSquare == 0) {
if (isOneExpressionOnly) {
this.iToken++;
break out;
}topLevel = true;
}break;
case 268437504:
nSquare++;
topLevel = false;
break;
case 268437505:
if (--nSquare == 0 && nParen == 0) {
if (isOneExpressionOnly) {
this.iToken++;
break out;
}topLevel = true;
}break;
}
} else {
var name = this.paramAsStr(i).toLowerCase();
var haveParens = (this.tokAt(i + 1) == 268435968);
if (!haveParens) {
if (this.chk) {
v = name;
} else if (localVars == null || (v = JU.PT.getMapValueNoCase(localVars, name)) == null && allContext) {
if (name.startsWith("_")) {
v = (name.equals("_") ? this.vwr.getModelSetAuxiliaryInfo() : name.equals("_m") ? this.vwr.getCurrentModelAuxInfo() : null);
}if (v == null) {
v = this.getContextVariableAsVariable(name, false);
if (v == null) {
switch (name) {
case "all":
v = this.vwr.bsA();
break;
case "this":
v = this.vwr.getFrameAtoms();
}
}} else if (ptEq == 0) {
this.invArg();
}}}if (v == null) {
if (JS.T.tokAttr(this.theTok, 1073741824) && this.isFunction(name)) {
if (!rpn.addOp(JS.SV.newV(134320141, this.theToken.value))) this.invArg();
if (!haveParens) {
rpn.addOp(JS.T.tokenLeftParen);
rpn.addOp(JS.T.tokenRightParen);
}} else {
$var = this.vwr.g.getAndSetNewVariable(name, false);
switch ($var.tok) {
case 2:
case 3:
if (this.noCopy(i, -1) || this.noCopy(i, 1)) break;
rpn.addXCopy($var);
continue;
default:
}
rpn.addX($var);
}}}}
if (v != null) {
if (Clazz.instanceOf(v,"JU.BS")) rpn.addXBs(v);
 else rpn.addXObj(v);
}}
var result = rpn.getResult();
if (result == null) {
if (!this.chk) rpn.dumpStacks("null result");
this.error(13);
}if (result.tok == 135198) {
if (isSpecialAssignment && ptEq == 0) {
var rv =  new JU.Lst();
rv.addLast( new JS.SV());
return rv;
}return result.value;
}if (this.chk) {
if (returnBoolean) return Boolean.TRUE;
if (returnString) return "";
} else {
if (returnBoolean) return Boolean.$valueOf(result.asBoolean());
if (returnString) {
if (result.tok == 4) result.intValue = 2147483647;
return result.asString();
}}switch (result.tok) {
case 1073742335:
case 1073742334:
return Boolean.$valueOf(result.intValue == 1);
case 2:
return Integer.$valueOf(result.intValue);
case 10:
case 3:
case 4:
case 8:
default:
return result.value;
}
}, "~N,~N,~S,~B,~B,~N,~B,java.util.Map,~S,~B");
Clazz.defineMethod(c$, "atomExpressionAt", 
function(index){
if (!this.checkToken(index)) {
this.iToken = index;
this.bad();
}return this.atomExpression(this.st, index, 0, true, false, null, true);
}, "~N");
Clazz.defineMethod(c$, "atomExpression", 
function(code, pcStart, pcStop, allowRefresh, allowUnderflow, ret, andNotDeleted){
this.isBondSet = false;
if (code !== this.st) {
this.tempStatement = this.st;
this.st = code;
}var rpn =  new JS.ScriptMathProcessor(this, false, false, false, ret == null, allowUnderflow, null);
var val;
var refreshed = false;
this.iToken = 1000;
var ignoreSubset = (pcStart < 0);
var isInMath = false;
var bs;
var nExpress = 0;
var ac = this.vwr.ms.ac;
var ptWithin = -10;
if (ignoreSubset) pcStart = -pcStart;
ignoreSubset = new Boolean (ignoreSubset | this.chk).valueOf();
if (pcStop == 0 && code.length > pcStart) pcStop = pcStart + 1;
expression_loop : for (var pc = pcStart; pc < pcStop; ++pc) {
this.iToken = pc;
var instruction = code[pc];
if (instruction == null) break;
var value = instruction.value;
switch (instruction.tok) {
case 1073742325:
pcStart = pc;
pcStop = code.length;
nExpress++;
break;
case 1073742326:
nExpress--;
if (nExpress > 0) continue;
break expression_loop;
case 1073742332:
if (this.isPoint3f(pc)) {
var pt = this.getPoint3f(pc, true, true);
if (pt != null) {
rpn.addXPt(pt);
pc = this.iToken;
break;
}}break;
case 1073742338:
if (pc > 0 && code[pc - 1].tok == 1073742332) rpn.addXBs( new JU.BS());
break;
case 268437504:
isInMath = true;
rpn.addOp(instruction);
break;
case 268437505:
isInMath = false;
rpn.addOp(instruction);
break;
case 12290:
rpn.addXBs(this.getAtomBitSet(value));
break;
case 7:
bs = JS.SV.getBitSet(instruction, false);
if (bs != null) {
rpn.addXBs(bs);
break;
}case 6:
rpn.addXBs(this.vwr.ms.getAtoms(1086324744, (instruction).asString()));
break;
case 134219777:
rpn.addX(JS.SV.newT(instruction));
rpn.addX(JS.SV.newV(9, this.hklParameter(pc + 2, null, true)));
pc = this.iToken;
break;
case 134217750:
rpn.addX(JS.SV.newT(instruction));
rpn.addX(JS.SV.newV(9, this.planeParameter(pc + 2, false)));
pc = this.iToken;
break;
case 1073742329:
rpn.addX(JS.SV.newT(instruction));
rpn.addXPt(this.getPoint3f(pc + 2, true, true));
pc = this.iToken;
break;
case 4:
var s = value;
if (s.indexOf("({") == 0) {
bs = JU.BS.unescape(s);
if (bs != null) {
rpn.addXBs(bs);
break;
}} else if (s.indexOf("|") >= 0 && ptWithin != pc - 4) {
rpn.addXBs(this.vwr.ms.getAtoms(1086324744, s));
break;
}rpn.addX(JS.SV.newT(instruction));
if (s.equals("hkl")) {
rpn.addX(JS.SV.newV(9, this.hklParameter(pc + 2, null, true)));
pc = this.iToken;
}break;
case 134217759:
ptWithin = pc;
case 134218757:
case 134218756:
case 1237320707:
case 134353926:
case 134217736:
case 268436992:
case 1275203608:
rpn.addOp(instruction);
break;
case 1073742327:
rpn.addXBs(this.vwr.getAllAtoms());
break;
case 1073742333:
rpn.addXBs( new JU.BS());
break;
case 1073742335:
case 1073742334:
rpn.addX(JS.SV.newT(instruction));
break;
case 1113589787:
rpn.addXBs(JU.BSUtil.copy(this.vwr.bsA()));
break;
case 2097194:
rpn.addXBs(JU.BSUtil.copy(this.vwr.slm.getHiddenSet()));
break;
case 12293:
rpn.addXBs(this.vwr.getMotionFixedAtoms(null, null));
break;
case 2097192:
rpn.addXBs(JU.BSUtil.copyInvert(this.vwr.slm.getHiddenSet(), ac));
break;
case 2097200:
rpn.addXBs(this.vwr.getBaseModelBitSet());
break;
case 2097198:
rpn.addXBs(this.chk ?  new JU.BS() : JU.BSUtil.copy(this.vwr.ms.getVisibleSet(!refreshed)));
refreshed = true;
break;
case 2097190:
if (!this.chk && allowRefresh) (this).refresh(false);
rpn.addXBs(this.chk ?  new JU.BS() : this.vwr.ms.getClickableSet(!allowRefresh));
allowRefresh = false;
break;
case 1073742356:
if (this.vwr.ms.mc != 1 || this.vwr.ms.haveBioModels) {
var atomID = instruction.intValue;
if (atomID > 0) {
bs = this.compareInt(1094713346, 268440324, atomID);
if (atomID == 2) bs.or(this.compareInt(1086326789, 268440324, 20));
rpn.addXBs(bs);
} else {
rpn.addXBs(this.getAtomBits(instruction.tok, value));
}} else {
rpn.addXBs((this).lookupIdentifierValue("_" + value));
}break;
case 2097155:
case 2097188:
case 2097156:
case 1612709894:
case 1073742331:
case 2097166:
case 2097165:
case 2097168:
case 2097170:
case 2097172:
case 2097174:
case 1073742360:
case 1073742355:
case 2097196:
case 1088421903:
case 1814695966:
rpn.addXBs(this.getAtomBits(instruction.tok, value));
break;
case 1073742358:
case 1073742359:
var iModel = instruction.intValue;
if (iModel == 2147483647 && Clazz.instanceOf(value, Integer)) {
iModel = (value).intValue();
if (!this.vwr.haveFileSet()) {
rpn.addXBs(this.getAtomBits(1073742358, Integer.$valueOf(iModel)));
break;
}if (iModel <= 2147) iModel = iModel * 1000000;
}rpn.addXBs(this.bitSetForModelFileNumber(iModel));
break;
case 1073742361:
case 1073742357:
rpn.addXBs(this.getAtomBits(instruction.tok, Integer.$valueOf(instruction.intValue)));
break;
case 1073742362:
if (isInMath) rpn.addXNum(instruction);
 else rpn.addXBs(this.getAtomBits(1073742362, Integer.$valueOf(JS.ScriptExpr.getSeqCode(instruction))));
break;
case 1073742363:
if (isInMath) {
rpn.addXNum(instruction);
rpn.addOp(JS.T.tokenMinus);
rpn.addXNum(code[++pc]);
break;
}var chainID = (pc + 3 < code.length && code[pc + 2].tok == 268439552 && code[pc + 3].tok == 1073742357 ? code[pc + 3].intValue : -1);
rpn.addXBs(this.getAtomBits(1073742363,  Clazz.newIntArray(-1, [JS.ScriptExpr.getSeqCode(instruction), JS.ScriptExpr.getSeqCode(code[++pc]), chainID])));
if (chainID != -1) pc += 2;
break;
case 1094713350:
case 1094713349:
rpn.addXBs(this.getAtomBits(instruction.tok, value));
break;
case 1073742340:
case 2097182:
rpn.addXBs(this.vwr.am.cmi < 0 ? this.vwr.getFrameAtoms() : this.vwr.getModelUndeletedAtomsBitSet(this.vwr.am.cmi));
break;
case 1612709900:
case 2097154:
case 1114249217:
case 1612709912:
case 136314895:
case 2097159:
case 2097160:
case 2097162:
case 2097178:
case 2097180:
rpn.addXBs((this).lookupIdentifierValue(value));
break;
case 268440323:
case 268440322:
case 268440321:
case 268440320:
case 268440324:
case 268440325:
case 268440326:
var tok = instruction.tok;
var tokWhat = instruction.intValue;
if ((tokWhat == 1094717448) && tok != 268440324) this.invArg();
var data = null;
if (tokWhat == 1715472409) {
if (pc + 2 == code.length) this.invArg();
if (!this.chk) data = this.vwr.getDataObj(code[++pc].value, null, 1);
}if (++pc == code.length) this.invArg();
rpn.addXBs(this.chk ?  new JU.BS() : this.getComparison(code[pc], tokWhat, tok, value, data));
break;
case 3:
case 2:
rpn.addXNum(instruction);
break;
case 10:
var bs1 = (Clazz.instanceOf(value,"JM.BondSet") ? value : JU.BSUtil.copy(value));
rpn.addXBs(bs1);
break;
case 8:
rpn.addXPt(value);
break;
default:
if (JS.T.tokAttr(instruction.tok, 268435456)) {
if (!rpn.addOp(instruction)) this.invArg();
break;
}if (!((typeof(value)=='string'))) {
rpn.addXObj(value);
break;
}val = this.getParameter(value, 0, true);
if (isInMath) {
rpn.addXObj(val);
break;
}if ((typeof(val)=='string') || Clazz.instanceOf(val,"JU.Lst")) val = this.getStringObjectAsVariable(val);
if ((typeof(val)=='string')) val = (this).lookupIdentifierValue(value);
rpn.addXObj(val);
break;
}
}
var expressionResult = rpn.getResult();
if (expressionResult == null) {
if (allowUnderflow) return null;
if (!this.chk) rpn.dumpStacks("after getResult");
this.error(13);
}var exp = expressionResult.value;
if ((typeof(exp)=='string') && (ret == null || (exp).startsWith("({"))) {
exp = (this.chk ?  new JU.BS() : this.getAtomBitSet(exp));
}if (ret != null && !(Clazz.instanceOf(exp,"JU.BS"))) {
ret[0] = exp;
return null;
}bs = (Clazz.instanceOf(exp,"JU.BS") ? exp :  new JU.BS());
this.isBondSet = (Clazz.instanceOf(exp,"JM.BondSet"));
if (!this.isBondSet && (bs = this.vwr.slm.excludeAtoms(bs, ignoreSubset)).length() > this.vwr.ms.ac) bs.clearAll();
if (this.tempStatement != null) {
this.st = this.tempStatement;
this.tempStatement = null;
}return bs;
}, "~A,~N,~N,~B,~B,~A,~B");
Clazz.defineMethod(c$, "getComparison", 
function(t, tokWhat, tokOp, strOp, data){
var tokValue = t.tok;
if (tokValue == 7) {
var bs =  new JU.BS();
if (tokOp != 268440324) bs.setBits(0, this.vwr.ms.ac);
var lst = (t).getList();
for (var i = lst.size(); --i >= 0; ) {
var res = this.getComparison(lst.get(i), tokWhat, tokOp, strOp, data);
if (tokOp == 268440324) bs.or(res);
 else bs.and(res);
}
return bs;
}var comparisonInt = t.intValue;
var comparisonFloat = NaN;
var isModel = (tokWhat == 1094717454);
var isIntProperty = JS.T.tokAttr(tokWhat, 1094713344);
var isFloatProperty = (JS.T.tokAttr(tokWhat, 1111490560) || (tokWhat & 1136656384) == 1077936128);
var isIntOrFloat = isIntProperty && isFloatProperty;
var isStringProperty = !isIntProperty && JS.T.tokAttr(tokWhat, 1086324736);
if (tokWhat == 1086326789) isIntProperty = !(isStringProperty = false);
var val = t.value;
if (JS.T.tokAttr(tokValue, 1073741824)) {
if ("_modelNumber".equalsIgnoreCase(val)) {
var modelIndex = this.vwr.am.cmi;
val = Integer.$valueOf(comparisonInt = (modelIndex < 0 ? 0 : this.vwr.getModelFileNumber(modelIndex)));
} else {
var v = this.getParameter(val, 1073742190, false);
if (v != null) {
if (v.tok == 7) return this.getComparison(v, tokWhat, tokOp, strOp, data);
comparisonInt = v.intValue;
val = (isStringProperty || tokWhat == 1094717448 && v.tok != 2 ? JS.SV.sValue(v) : JS.SV.nValue(v));
t = v;
}}}if (Clazz.instanceOf(val,"JU.P3")) {
if (tokWhat == 1765808134) {
comparisonInt = JU.CU.colorPtToFFRGB(val);
tokValue = 2;
isIntProperty = true;
}} else if ((typeof(val)=='string')) {
if (tokWhat == 1765808134) {
comparisonInt = JU.CU.getArgbFromString(val);
if (comparisonInt == 0 && JS.T.tokAttr(tokValue, 1073741824)) {
val = this.getVarParameter(val, true);
if ((val).startsWith("{")) {
val = JU.Escape.uP(val);
if (Clazz.instanceOf(val,"JU.P3")) comparisonInt = JU.CU.colorPtToFFRGB(val);
 else comparisonInt = 0;
} else {
comparisonInt = JU.CU.getArgbFromString(val);
}}tokValue = 2;
isIntProperty = true;
} else if (!isStringProperty) {
if (tokWhat == 1094717448) {
val = Integer.$valueOf(t.tok == 2 ? t.intValue : -1000 - (val + " ").codePointAt(0));
} else if (tokWhat == 1639976963 || tokWhat == 1237320707 || tokWhat == 1086326789) isStringProperty = !(isIntProperty = (comparisonInt != 2147483647));
 else val = JS.SV.nValue(t);
if (Clazz.instanceOf(val, Integer)) comparisonFloat = comparisonInt = (val).intValue();
 else if (Clazz.instanceOf(val, Float) && isModel) comparisonInt = JM.ModelSet.modelFileNumberFromFloat((val).floatValue());
}}if (isStringProperty && !((typeof(val)=='string'))) {
val = "" + val;
}if (Clazz.instanceOf(val, Integer) || tokValue == 2) {
if (isModel) {
if (comparisonInt >= 1000000) tokWhat = -1094717454;
} else if (isIntOrFloat) {
isFloatProperty = false;
} else if (isFloatProperty) {
comparisonFloat = comparisonInt;
}} else if (Clazz.instanceOf(val, Float)) {
if (isModel) {
tokWhat = -1094717454;
} else {
comparisonFloat = (val).floatValue();
if (isIntOrFloat) {
isIntProperty = false;
} else if (isIntProperty) {
comparisonInt = Clazz.floatToInt(comparisonFloat);
}}} else if (!isStringProperty) {
this.iToken++;
this.invArg();
}if (isModel && comparisonInt >= 1000000 && comparisonInt % 1000000 == 0) {
comparisonInt /= 1000000;
tokWhat = 1228935687;
isModel = false;
}if (tokWhat == -1094717454 && tokOp == 268440324) {
return this.bitSetForModelFileNumber(comparisonInt);
}if (strOp != null && strOp.indexOf("-") >= 0) {
if (isIntProperty) comparisonInt = -comparisonInt;
 else if (!Float.isNaN(comparisonFloat)) comparisonFloat = -comparisonFloat;
}return (isIntProperty ? this.compareInt(tokWhat, tokOp, comparisonInt) : isStringProperty ? this.compareString(tokWhat, tokOp, val) : this.compareFloatData(tokWhat, data, tokOp, comparisonFloat));
}, "JS.T,~N,~N,~S,~A");
Clazz.defineMethod(c$, "noCopy", 
function(i, dir){
switch (this.tokAt(i + dir)) {
case 268441602:
case 268441601:
return ((this.st[i + dir].intValue == -1) == (dir == -1));
default:
return false;
}
}, "~N,~N");
Clazz.defineMethod(c$, "getAssocArray", 
function(i){
var ht =  new java.util.Hashtable();
var closer = (this.tokAt(i) == 1073742332 ? 1073742338 : 268437505);
for (i = i + 1; i < this.slen; i++) {
var tok = this.tokAt(i);
if (tok == closer) break;
var key = null;
if (Clazz.instanceOf(this.st[i],"JS.SV")) key = (this.st[i]).myName;
if (key == null) key = JS.SV.sValue(this.st[i]);
i++;
if (this.tokAt(i++) != 268436482) this.invArg();
var v = this.parameterExpression(i, 0, null, false, true, -1, false, null, null, false);
if (v.size() == 0) this.invArg();
ht.put(key, JS.SV.copySafely(v.get(0)));
i = this.iToken;
if (this.tokAt(i) != 268436992) break;
}
this.iToken = i;
if (this.tokAt(i) != closer) this.invArg();
return ht;
}, "~N");
Clazz.defineMethod(c$, "listBS", 
function(bs){
var l =  new JU.Lst();
l.addLast(JS.SV.newV(10, bs));
return l;
}, "JU.BS");
Clazz.defineMethod(c$, "compareFloatData", 
function(tokWhat, data, tokOperator, comparisonFloat){
var bs =  new JU.BS();
var ac = this.vwr.ms.ac;
var modelSet = this.vwr.ms;
var atoms = modelSet.at;
var propertyFloat = 0;
this.vwr.autoCalculate(tokWhat, null);
var isProp = (tokWhat == 1715472409);
if (!isProp && this.ptTemp == null) this.ptTemp =  new JU.P3();
for (var i = ac; --i >= 0; ) {
var match = false;
var atom = atoms[i];
if (JM.AtomCollection.isDeleted(atom)) continue;
if (isProp) {
if (data == null || data.length <= i) continue;
propertyFloat = data[i];
} else {
propertyFloat = atom.atomPropertyFloat(this.vwr, tokWhat, this.ptTemp);
}match = this.compareFloat(tokOperator, propertyFloat, comparisonFloat);
if (match) bs.set(i);
}
return bs;
}, "~N,~A,~N,~N");
Clazz.defineMethod(c$, "compareFloat", 
function(tokOperator, a, b){
if ((a == a) != (b == b)) return (tokOperator == 268440325);
switch (tokOperator) {
case 268440323:
return a < b;
case 268440322:
return a <= b || a != a;
case 268440321:
return a >= b || a != a;
case 268440320:
return a > b;
case 268440324:
return a == b || a != a;
case 268440325:
return a != b && a == a;
}
return false;
}, "~N,~N,~N");
Clazz.defineMethod(c$, "compareString", 
function(tokWhat, tokOperator, comparisonString){
var bs =  new JU.BS();
var atoms = this.vwr.ms.at;
var ac = this.vwr.ms.ac;
var isCaseSensitive = (tokOperator == 268440326 || tokWhat == 1086326788 && this.vwr.getBoolean(603979822));
if (!isCaseSensitive) comparisonString = comparisonString.toLowerCase();
for (var i = ac; --i >= 0; ) {
if (atoms[i] == null) continue;
var propertyString = atoms[i].atomPropertyString(this.vwr, tokWhat);
if (!isCaseSensitive) propertyString = propertyString.toLowerCase();
if (this.compareStringValues(tokOperator, propertyString, comparisonString)) bs.set(i);
}
return bs;
}, "~N,~N,~S");
Clazz.defineMethod(c$, "compareStringValues", 
function(tokOperator, propertyValue, comparisonValue){
switch (tokOperator) {
case 268440324:
case 268440325:
return (JU.PT.isMatch(propertyValue, comparisonValue, true, true) == (tokOperator == 268440324));
case 268440326:
return JU.PT.isLike(propertyValue, comparisonValue);
default:
this.invArg();
}
return false;
}, "~N,~S,~S");
Clazz.defineMethod(c$, "compareInt", 
function(tokWhat, tokOperator, ival){
var ia = 2147483647;
var propertyBitSet = null;
var bitsetComparator = tokOperator;
var bitsetBaseValue = ival;
var modelSet = this.vwr.ms;
var atoms = modelSet.at;
var ac = modelSet.ac;
var imax = -1;
var imin = 0;
var iModel = -1;
var cellRange = null;
var nOps = 0;
var bs;
switch (tokWhat) {
case 1296041985:
switch (bitsetComparator) {
case 268440321:
case 268440320:
imax = 2147483647;
break;
}
break;
case 1094713347:
try {
switch (tokOperator) {
case 268440323:
return JU.BSUtil.newBitSet2(0, ival);
case 268440322:
return JU.BSUtil.newBitSet2(0, ival + 1);
case 268440321:
return JU.BSUtil.newBitSet2(ival, ac);
case 268440320:
return JU.BSUtil.newBitSet2(ival + 1, ac);
case 268440324:
return (ival < ac ? JU.BSUtil.newBitSet2(ival, ival + 1) :  new JU.BS());
case 268440325:
default:
bs = JU.BSUtil.setAll(ac);
if (ival >= 0) bs.clear(ival);
return bs;
}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return  new JU.BS();
} else {
throw e;
}
}
}
bs = JU.BS.newN(ac);
for (var i = 0; i < ac; ++i) {
var match = false;
var atom = atoms[i];
if (JM.AtomCollection.isDeleted(atom)) continue;
switch (tokWhat) {
default:
ia = atom.atomPropertyInt(tokWhat);
break;
case 1094713368:
case 1094717448:
return JU.BSUtil.copy(this.vwr.ms.getConformation(-1, ival, false, null));
case 1296041985:
propertyBitSet = atom.atomSymmetry;
if (propertyBitSet == null) continue;
if (atom.mi != iModel) {
iModel = atom.mi;
cellRange = modelSet.getModelCellRange(iModel);
nOps = modelSet.getModelSymmetryCount(iModel);
}if (bitsetBaseValue >= 200) {
if (cellRange == null) continue;
ival = bitsetBaseValue % 1000;
var symop = Clazz.doubleToInt(bitsetBaseValue / 1000) - 1;
if (symop < 0) {
match = true;
} else if (nOps == 0 || symop >= 0 && !(match = propertyBitSet.get(symop))) {
continue;
}bitsetComparator = 1073742333;
if (symop < 0) ia = atom.getCellTranslation(ival, cellRange, nOps);
 else ia = atom.getSymmetryTranslation(symop, cellRange, nOps);
} else if (nOps > 0) {
if (ival > nOps) {
if (bitsetComparator != 268440323 && bitsetComparator != 268440322) continue;
}if (bitsetComparator == 268440325) {
if (ival > 0 && ival <= nOps && !propertyBitSet.get(ival)) {
bs.set(i);
}continue;
}var bs1 = JU.BSUtil.copy(propertyBitSet);
bs1.clearBits(nOps, bs1.length());
propertyBitSet = bs1;
}switch (bitsetComparator) {
case 268440323:
imax = ival - 1;
break;
case 268440322:
imax = ival;
break;
case 268440321:
imin = ival - 1;
break;
case 268440320:
imin = ival;
break;
case 268440324:
imax = ival;
imin = ival - 1;
break;
case 268440325:
match = !propertyBitSet.get(ival);
break;
}
if (imin < 0) imin = 0;
if (imin < imax) {
var pt = propertyBitSet.nextSetBit(imin);
if (pt >= 0 && pt < imax) match = true;
}if (!match || ia == 2147483647) tokOperator = 1073742333;
}
switch (tokOperator) {
case 1073742333:
break;
case 268440323:
match = (ia < ival);
break;
case 268440322:
match = (ia <= ival);
break;
case 268440321:
match = (ia >= ival);
break;
case 268440320:
match = (ia > ival);
break;
case 268440324:
match = (ia == ival);
break;
case 268440325:
match = (ia != ival);
break;
}
if (match) bs.set(i);
}
return bs;
}, "~N,~N,~N");
Clazz.defineMethod(c$, "getBitsetPropertySelector", 
function(i, xTok){
var tok = this.getToken(i).tok;
switch (tok) {
case 1275068725:
case 32:
case 64:
case 96:
case 192:
case 128:
case 160:
case 1715472409:
break;
default:
if (JS.T.tokAttrOr(tok, 1077936128, 1140850688) || xTok == 6) break;
if (tok != 805307393 && !JS.T.tokAttr(tok, 1073741824)) break;
var name = this.paramAsStr(i);
if (this.isFunction(name.toLowerCase())) {
tok = 134320141;
break;
}}
return JS.SV.newSV(268442113, tok, this.paramAsStr(i));
}, "~N,~N");
Clazz.defineMethod(c$, "getBitsetProperty", 
function(bs, pts, tok, ptRef, planeRef, tokenValue, opValue, useAtomMap, index, asVectorIfAll){
var haveIndex = (index != 2147483647);
var isAtoms = haveIndex || !(Clazz.instanceOf(tokenValue,"JM.BondSet")) && !(Clazz.instanceOf(bs,"JM.BondSet"));
var minmaxtype = tok & 480;
var selectedFloat = (minmaxtype == 224);
var isPivot = (minmaxtype == 288);
if (isPivot) minmaxtype = 480;
var ac = this.vwr.ms.ac;
var fout = (minmaxtype == 256 ?  Clazz.newFloatArray (ac, 0) : null);
var isExplicitlyAll = (minmaxtype == 480 || selectedFloat);
tok &= -481;
var info = null;
if (tok == 0) tok = (isAtoms ? 1153433601 : 1677721602);
var isPt = false;
var isHash = false;
var isInt = false;
var isString = false;
switch (tok) {
case 1275068446:
return (this.vwr.getModelSetAuxiliaryInfoForAtoms(bs)).get("models");
case 1145047049:
case 1145047055:
case 1145047050:
case 1145047053:
case 1145045008:
case 1145045006:
case 1765808134:
case 1145047052:
isPt = true;
break;
case 1275203608:
isHash = true;
info =  Clazz.newArray(-1, [null, null]);
break;
case 134320141:
case 1275069443:
break;
case 1145045003:
isString = true;
break;
case 1086324754:
isInt = (tokenValue === "color");
isString = !isInt;
break;
default:
isInt = JS.T.tokAttr(tok, 1094713344) && !JS.T.tokAttr(tok, 1111490560);
isString = !isInt && JS.T.tokAttr(tok, 1086324736);
}
var pt = (isPt || !isAtoms ?  new JU.P3() : null);
if (isExplicitlyAll || isString && !haveIndex && minmaxtype != 256 && minmaxtype != 32) minmaxtype = 1073742327;
var vout = (minmaxtype == 1073742327 ?  new JU.Lst() : null);
var bsNew = null;
var userFunction = null;
var params = null;
var bsAtom = null;
var tokenAtom = null;
var ptT = null;
var data = null;
var ffdata = null;
switch (tok) {
case 1153433601:
if (isAtoms) break;
case 1677721602:
if (this.chk) return bs;
bsNew = (tok == 1153433601 ? this.vwr.ms.getAtoms(1677721602, bs) : (isAtoms ? JM.BondSet.newBS(this.vwr.getBondsForSelectedAtoms(bs)) : bs));
var i;
switch (minmaxtype) {
case 32:
i = bsNew.nextSetBit(0);
break;
case 64:
i = bsNew.length() - 1;
break;
case 192:
case 128:
case 160:
return Float.$valueOf(NaN);
default:
return bsNew;
}
bsNew.clearAll();
if (i >= 0) bsNew.set(i);
return bsNew;
case 1086324745:
switch (minmaxtype) {
case 0:
case 32:
case 1073742327:
return this.getCmdExt().getBitsetIdent(bs, null, tokenValue, useAtomMap, index, isExplicitlyAll);
}
return "";
case 134320141:
userFunction = (opValue)[0];
params = (opValue)[1];
bsAtom = JU.BS.newN(ac);
tokenAtom = JS.SV.newV(10, bsAtom);
break;
case 1111490587:
for (var j = fout.length; --j >= 0; ) fout[j] = NaN;

case 1111490574:
case 1111490575:
this.vwr.autoCalculate(tok, tokenValue);
break;
case 1275069443:
if (ptRef == null && planeRef == null) return  new JU.P3();
break;
case 1765808134:
ptT =  new JU.P3();
break;
case 1715472409:
data = this.vwr.getDataObj(opValue, null, 1);
if (data == null) ffdata = this.vwr.getDataObj(opValue, null, 2);
if (ffdata != null) {
minmaxtype = 1073742327;
vout =  new JU.Lst();
}break;
}
var n = 0;
var ivMinMax = 0;
var fvMinMax = 0;
var sum = 0;
var sum2 = 0;
switch (minmaxtype) {
case 32:
ivMinMax = 2147483647;
fvMinMax = 3.4028235E38;
break;
case 64:
ivMinMax = -2147483648;
fvMinMax = -3.4028235E38;
break;
}
var modelSet = this.vwr.ms;
var mode = (ffdata != null ? 5 : isHash ? 4 : isPt ? 3 : isString ? 2 : isInt ? 1 : 0);
if (isAtoms) {
var haveBitSet = (bs != null);
var i0;
var i1;
if (pts != null) {
i0 = 0;
i1 = pts.size();
} else if (haveIndex) {
i0 = index;
i1 = index + 1;
} else if (haveBitSet) {
i0 = bs.nextSetBit(0);
i1 = Math.min(ac, bs.length());
} else {
i0 = 0;
i1 = ac;
}if (this.chk) i1 = 0;
for (var i = i0; i >= 0 && i < i1; i = (haveBitSet ? bs.nextSetBit(i + 1) : i + 1)) {
n++;
var atom;
if (pts == null) {
atom = modelSet.at[i];
if (JM.AtomCollection.isDeleted(atom)) continue;
} else {
atom = null;
}switch (mode) {
case 0:
var fv = 3.4028235E38;
switch (tok) {
case 134320141:
bsAtom.set(i);
fv = JS.SV.fValue((this).getUserFunctionResult(userFunction, params, tokenAtom));
bsAtom.clear(i);
break;
case 1715472409:
fv = (data == null || i >= data.length ? 0 : data[i]);
break;
case 1275069443:
if (planeRef != null) fv = JU.Measure.distanceToPlane(planeRef, atom);
 else fv = (pts != null ? JS.SV.ptValue(pts.get(i)).distance(ptRef) : atom !== ptRef || minmaxtype != 32 ? atom.distance(ptRef) : NaN);
break;
default:
fv = atom.atomPropertyFloat(this.vwr, tok, this.ptTemp);
}
if (fv == 3.4028235E38 || Float.isNaN(fv) && minmaxtype != 1073742327) {
n--;
continue;
}switch (minmaxtype) {
case 32:
if (fv < fvMinMax) fvMinMax = fv;
break;
case 64:
if (fv > fvMinMax) fvMinMax = fv;
break;
case 256:
fout[i] = fv;
break;
case 1073742327:
vout.addLast(Float.$valueOf(fv));
break;
case 160:
case 192:
sum2 += (fv) * fv;
case 128:
default:
sum += fv;
}
break;
case 1:
var iv = 0;
switch (tok) {
case 1094717448:
case 1094713349:
this.errorStr(45, JS.T.nameOf(tok));
break;
case 1086324754:
iv = (atom.getWyckoffPosition(false).charAt(0)).charCodeAt(0);
switch (iv) {
case 63:
iv = 0;
break;
case 65:
iv = 27;
break;
default:
iv = iv & 0x1F;
break;
}
break;
default:
iv = atom.atomPropertyInt(tok);
break;
}
switch (minmaxtype) {
case 32:
if (iv < ivMinMax) ivMinMax = iv;
break;
case 64:
if (iv > ivMinMax) ivMinMax = iv;
break;
case 256:
fout[i] = iv;
break;
case 1073742327:
vout.addLast(Integer.$valueOf(iv));
break;
case 160:
case 192:
sum2 += (iv) * iv;
case 128:
default:
sum += iv;
}
break;
case 2:
var s = atom.atomPropertyString(this.vwr, tok);
switch (minmaxtype) {
case 256:
fout[i] = JU.PT.parseFloat(s);
break;
default:
if (vout == null) return s;
vout.addLast(s);
}
break;
case 3:
var t = atom.atomPropertyTuple(this.vwr, tok, this.ptTemp);
switch (minmaxtype) {
case 256:
fout[i] = (pt == null ? -1 : t == null ? 0 : t.length());
break;
case 1073742327:
vout.addLast(t == null ? Integer.$valueOf(-1) : JU.P3.newP(t));
break;
default:
if (t == null) n--;
 else pt.add(t);
}
break;
case 4:
switch (tok) {
case 1275203608:
info[0] = Integer.$valueOf(i);
info[1] = "";
this.vwr.shm.getShapePropertyData(21, "info", info);
if (info[1] != null) {
if (vout == null) return info[1];
vout.addLast(info[1]);
}break;
}
break;
case 5:
vout.addLast(ffdata[i]);
break;
}
if (haveIndex) break;
}
} else {
var isAll = (bs == null);
var i0 = (isAll ? 0 : bs.nextSetBit(0));
var i1 = this.vwr.ms.bondCount;
for (var i = i0; i >= 0 && i < i1; i = (isAll ? i + 1 : bs.nextSetBit(i + 1))) {
var bond = modelSet.bo[i];
if (bond == null) continue;
n++;
switch (tok) {
case 1140850691:
var fv = bond.atom1.distance(bond.atom2);
switch (minmaxtype) {
case 32:
if (fv < fvMinMax) fvMinMax = fv;
break;
case 64:
if (fv > fvMinMax) fvMinMax = fv;
break;
case 1073742327:
vout.addLast(Float.$valueOf(fv));
break;
case 160:
case 192:
sum2 += fv * fv;
case 128:
default:
sum += fv;
}
break;
case 1145047049:
switch (minmaxtype) {
case 1073742327:
pt.ave(bond.atom1, bond.atom2);
vout.addLast(JU.P3.newP(pt));
break;
default:
pt.add(bond.atom1);
pt.add(bond.atom2);
n++;
}
break;
case 1765808134:
JU.CU.colorPtFromInt(this.vwr.gdata.getColorArgbOrGray(bond.colix), ptT);
switch (minmaxtype) {
case 1073742327:
vout.addLast(JU.P3.newP(ptT));
break;
default:
pt.add(ptT);
}
break;
default:
this.errorStr(46, JS.T.nameOf(tok));
}
}
}if (minmaxtype == 256) return fout;
if (minmaxtype == 1073742327) {
if (asVectorIfAll) {
if (isPivot) {
return this.getMathExt().getMinMax(vout, 1275068725, false);
}return vout;
}var len = vout.size();
if ((isString || isHash) && !isExplicitlyAll && len == 1) return vout.get(0);
if (selectedFloat) {
fout =  Clazz.newFloatArray (len, 0);
for (var i = len; --i >= 0; ) {
var v = vout.get(i);
switch (mode) {
case 0:
fout[i] = (v).floatValue();
break;
case 1:
fout[i] = (v).floatValue();
break;
case 2:
fout[i] = JU.PT.parseFloat(v);
break;
case 3:
fout[i] = (v == null ? -1 : (v).length());
break;
}
}
return fout;
}if (tok == 1086324744) {
var sb =  new JU.SB();
for (var i = 0; i < len; i++) sb.append(vout.get(i));

return sb.toString();
}var sout =  new Array(len);
for (var i = len; --i >= 0; ) {
var v = vout.get(i);
if (Clazz.instanceOf(v,"JU.P3")) sout[i] = JU.Escape.eP(v);
 else sout[i] = "" + vout.get(i);
}
return sout;
}if (isPt) return (n == 0 ? Integer.$valueOf(-1) : JU.P3.new3(pt.x / n, pt.y / n, pt.z / n));
if (isHash) return  new java.util.Hashtable();
if (n == 0 || n == 1 && minmaxtype == 192) return Float.$valueOf(NaN);
if (isInt) {
switch (minmaxtype) {
case 32:
case 64:
return Integer.$valueOf(ivMinMax);
case 160:
case 192:
break;
case 128:
return Integer.$valueOf(Clazz.doubleToInt(sum));
default:
if (sum / n == Clazz.doubleToInt(sum / n)) return Integer.$valueOf(Clazz.doubleToInt(sum / n));
return Float.$valueOf((sum / n));
}
}switch (minmaxtype) {
case 32:
case 64:
sum = fvMinMax;
break;
case 128:
break;
case 160:
sum = sum2;
break;
case 192:
sum = Math.sqrt((sum2 - sum * sum / n) / (n - 1));
break;
default:
sum /= n;
break;
}
return Float.$valueOf(sum);
}, "JU.BS,JU.Lst,~N,JU.P3,JU.P4,~O,~O,~B,~N,~B");
Clazz.defineMethod(c$, "bitSetForModelFileNumber", 
function(m){
var bs = JU.BS.newN(this.vwr.ms.ac);
if (this.chk) return bs;
var modelCount = this.vwr.ms.mc;
var haveFileSet = this.vwr.haveFileSet();
if (m < 1000000 && haveFileSet) m *= 1000000;
var pt = m % 1000000;
if (pt == 0) {
var model1 = this.vwr.ms.getModelNumberIndex(m + 1, false, false);
if (model1 < 0) return bs;
var model2 = (m == 0 ? modelCount : this.vwr.ms.getModelNumberIndex(m + 1000001, false, false));
if (model1 < 0) model1 = 0;
if (model2 < 0) model2 = modelCount;
if (this.vwr.ms.isTrajectory(model1)) model2 = model1 + 1;
for (var j = model1; j < model2; j++) bs.or(this.vwr.getModelUndeletedAtomsBitSet(j));

} else {
var modelIndex = this.vwr.ms.getModelNumberIndex(m, false, true);
if (modelIndex >= 0) bs.or(this.vwr.getModelUndeletedAtomsBitSet(modelIndex));
}return bs;
}, "~N");
Clazz.defineMethod(c$, "getStringObjectAsVariable", 
function(obj){
if (obj == null) return obj;
if ((typeof(obj)=='string')) {
var s = obj;
if (s.length == 0) return s;
return JS.SV.unescapePointOrBitsetAsVariable(s);
}var lst = obj;
if (lst.size() == 0) return "";
var v0 = lst.get(0);
if (JS.SV.ptValue(v0) != null) return obj;
if (lst.get(0).asString().contains("|")) return this.vwr.ms.getAtoms(1086324744, JS.SV.newV(7, lst).asString());
var bs = JS.SV.unEscapeBitSetArray(lst, true);
return (bs == null ? "" : bs);
}, "~O");
Clazz.defineMethod(c$, "getAtomBits", 
function(tokType, specInfo){
return (this.chk ?  new JU.BS() : this.vwr.ms.getAtoms(tokType, specInfo));
}, "~N,~O");
c$.getSeqCode = Clazz.defineMethod(c$, "getSeqCode", 
function(instruction){
return (instruction.intValue == 2147483647 ? (instruction.value).intValue() : JM.Group.getSeqcodeFor(instruction.intValue, ' '));
}, "JS.T");
Clazz.defineMethod(c$, "setVariable", 
function(pt, ptMax, key, isSet){
var bs = null;
var propertyName = "";
var settingData = key.startsWith("property_");
var isThrown = key.equals("thrown_value");
var isExpression = (this.tokAt(1) == 1073742325 || this.tokAt(1) == 268435968);
var t = (settingData ? null : key.length == 0 ?  new JS.SV() : this.getContextVariableAsVariable(key, false));
if (isSet && !isExpression) {
switch (this.tokAt(2)) {
default:
pt = 2;
break;
case 268440324:
pt = 3;
break;
case 1073742195:
case 268437504:
if (this.st[0].intValue == 61) {
pt = 2;
break;
}case 1073742336:
case 1073742337:
key = null;
break;
}
}var nv = 0;
var v = this.parameterExpression(pt, ptMax, key, true, true, -1, false, null, null, isSet && pt == 1);
nv = v.size();
if (nv == 0) this.invArg();
if (this.chk || v.get(0).tok == 0) return null;
var tv = JS.SV.selectItemVar(JS.SV.copySafely(v.get(nv - 1)));
if (nv > 1) {
var sel = (nv > 2 ? v.get(1) : null);
t = v.get(0);
var selectOne = false;
switch (t.tok) {
case 6:
case 14:
if (nv > 3) this.invArg();
t.mapPut(sel.asString(), tv);
break;
case 7:
if (nv > 2 + (sel == null ? 0 : 1)) this.invArg();
if (sel == null) {
sel = t;
} else {
t = JS.SV.selectItemVar(t);
}selectOne = true;
break;
case 4:
if (sel.tok != 2) {
t.value = JU.PT.rep(t.asString(), sel.asString(), tv.asString());
t.intValue = 2147483647;
break;
}case 11:
case 12:
if (t.intValue == 2147483647) selectOne = true;
 else t.setSelectedValue(t.intValue, sel.asInt(), tv);
break;
case 8:
var p = (t.value = JU.P3.newP(t.value));
var f = tv.asFloat();
switch (JS.T.getTokFromName(sel.asString())) {
case 1111492629:
p.x = f;
break;
case 1111492630:
p.y = f;
break;
case 1111492631:
p.z = f;
break;
}
break;
case 10:
bs = JS.SV.getBitSet(t, true);
var nAtoms = this.vwr.ms.ac;
var nbs = bs.cardinality();
propertyName = sel.asString();
var tok = JS.T.getTokFromName(propertyName);
switch (tok) {
case 0:
if (propertyName.startsWith("property_")) {
var obj;
if (tv.tok == 7) {
var nmin = (tv.getList().size() == nbs ? nbs : nAtoms);
obj = (JS.SV.getArrayDepth(tv) > 1 ? JS.SV.fflistValue(tv, nmin) : JS.SV.flistValue(tv, nmin));
} else {
obj = tv.asString();
}this.vwr.setData(propertyName,  Clazz.newArray(-1, [propertyName, obj, JU.BSUtil.copy(bs), Integer.$valueOf(-1)]), nAtoms, 0, 0, tv.tok == 7 ? 2147483647 : -2147483648, 0);
break;
}this.iToken = pt;
this.error(56);
break;
case 1825200146:
case 1287653388:
this.vwr.shm.loadShape(5);
default:
this.setBitsetProperty(bs, tok, tv.asInt(), tv.asFloat(), tv);
break;
}
break;
}
if (selectOne) t.setSelectedValue(sel.intValue, 2147483647, tv);
return null;
}var needVariable = (!settingData && t == null && (isThrown || !((typeof(tv.value)=='string') || tv.tok == 2 || Clazz.instanceOf(tv.value, Integer) || Clazz.instanceOf(tv.value, Float) || Clazz.instanceOf(tv.value, Boolean))));
if (needVariable && key != null) {
if (key.startsWith("_") || (t = this.vwr.g.getAndSetNewVariable(key, true)) == null) this.errorStr(22, key);
}if (t != null) return t.setv(tv);
var vv = JS.SV.oValue(tv);
if (settingData) {
if (tv.tok == 7) vv = tv.asString();
this.vwr.setData(key,  Clazz.newArray(-1, [key, "" + vv, JU.BSUtil.copy(this.vwr.bsA()), Integer.$valueOf(0)]), this.vwr.ms.ac, 0, 0, -2147483648, 0);
return null;
}if (Clazz.instanceOf(vv, Boolean)) {
this.setBooleanProperty(key, (vv).booleanValue());
} else if (Clazz.instanceOf(vv, Integer)) {
this.setIntProperty(key, (vv).intValue());
} else if (Clazz.instanceOf(vv, Float)) {
this.setFloatProperty(key, (vv).floatValue());
} else if ((typeof(vv)=='string')) {
this.setStringProperty(key, vv);
} else {
}return tv;
}, "~N,~N,~S,~B");
Clazz.defineMethod(c$, "setBitsetProperty", 
function(bs, tok, iValue, fValue, tokenValue){
if (this.chk || bs.isEmpty()) return;
var list = null;
var sValue = null;
var fvalues = null;
var pt;
var sv = null;
var nValues = 0;
var isStrProperty = JS.T.tokAttr(tok, 1086324736);
if (tokenValue.tok == 7) {
sv = (tokenValue).getList();
if ((nValues = sv.size()) == 0) return;
}switch (tok) {
case 1145047049:
case 1145047050:
case 1145047053:
case 1145047055:
switch (tokenValue.tok) {
case 8:
this.vwr.setAtomCoords(bs, tok, tokenValue.value);
break;
case 7:
this.theToken = tokenValue;
this.vwr.setAtomCoords(bs, tok, this.getPointArray(-1, nValues, true, true));
break;
}
return;
case 1765808134:
var value = null;
var prop = "color";
switch (tokenValue.tok) {
case 7:
var values =  Clazz.newIntArray (nValues, 0);
for (var i = nValues; --i >= 0; ) {
var svi = sv.get(i);
pt = JS.SV.ptValue(svi);
if (pt != null) {
values[i] = JU.CU.colorPtToFFRGB(pt);
} else if (svi.tok == 2) {
values[i] = svi.intValue;
} else {
values[i] = JU.CU.getArgbFromString(svi.asString());
if (values[i] == 0) values[i] = svi.asInt();
}if (values[i] == 0) this.errorStr2(50, "ARRAY", svi.asString());
}
value = values;
prop = "colorValues";
break;
case 8:
value = Integer.$valueOf(JU.CU.colorPtToFFRGB(tokenValue.value));
break;
case 4:
value = tokenValue.value;
break;
default:
value = Integer.$valueOf(JS.SV.iValue(tokenValue));
break;
}
(this).setAtomProp(prop, value, bs);
return;
case 1825200146:
case 1287653388:
if (tokenValue.tok != 7) sValue = JS.SV.sValue(tokenValue);
break;
case 1086326789:
case 1094715402:
(this).clearDefinedVariableAtomSets();
isStrProperty = false;
break;
}
switch (tokenValue.tok) {
case 7:
if (isStrProperty) list = JS.SV.strListValue(tokenValue);
 else fvalues = JS.SV.flistValue(tokenValue, nValues);
break;
case 4:
if (sValue == null) list = JU.PT.getTokens(JS.SV.sValue(tokenValue));
break;
}
if (list != null) {
nValues = list.length;
if (!isStrProperty) {
fvalues =  Clazz.newFloatArray (nValues, 0);
for (var i = nValues; --i >= 0; ) fvalues[i] = (tok == 1086326789 ? JU.Elements.elementNumberFromSymbol(list[i], false) : JU.PT.parseFloat(list[i]));

}if (tokenValue.tok != 7 && nValues == 1) {
if (isStrProperty) sValue = list[0];
 else fValue = fvalues[0];
iValue = Clazz.floatToInt(fValue);
list = null;
fvalues = null;
}}if (!JS.T.tokAttr(tok, 2048)) this.error(56);
this.vwr.setAtomProperty(bs, tok, iValue, fValue, sValue, fvalues, list);
}, "JU.BS,~N,~N,~N,JS.T");
Clazz.defineMethod(c$, "setStatement", 
function(st0, pt0){
this.st = st0;
this.slen = this.st.length;
if (this.slen == 0) return true;
var fixed;
var i;
var tok;
for (i = pt0; i < this.slen; i++) {
if (this.st[i] == null) {
this.slen = i;
return true;
}if (this.st[i].tok == 12290) break;
}
if (i == this.slen || this.chk) return i == this.slen;
switch (this.st[0].tok) {
case 102436:
case 134320141:
case 1073741824:
if (this.tokAt(1) == 268435968) return true;
}
fixed =  new Array(this.slen);
fixed[0] = this.st[0];
var isExpression = false;
var j = pt0;
for (i = pt0; i < this.slen; i++) {
if (this.st[i] == null) continue;
switch (tok = this.getToken(i).tok) {
default:
fixed[j] = this.st[i];
break;
case 1073742325:
case 1073742326:
isExpression = (tok == 1073742325);
fixed[j] = this.st[i];
break;
case 12290:
if (++i == this.slen) this.invArg();
var v;
var forceString = (this.theToken.intValue == 4);
var s;
var $var = this.paramAsStr(i);
var isClauseDefine = (this.tokAt(i) == 1073742325);
var isSetAt = (pt0 == 1 && j == 1 && this.st[0] === JS.T.tokenSetCmd);
if (isClauseDefine) {
var vt = this.parameterExpressionToken(++i);
if (this.chk) {
v = null;
} else if (vt.tok != 7) {
v = JS.SV.oValue(vt);
} else if (!isExpression) {
v = vt;
} else {
var bs = JS.SV.getBitSet(vt, true);
if (bs == null) {
var sv = JS.SV.sValue(vt);
v = (sv.indexOf("|") < 0 ? this.getAtomBitSet(sv) : sv);
} else {
v = bs;
}}i = this.iToken;
} else if (this.chk) {
v =  new JU.BS();
} else {
if (this.tokAt(i) == 2) {
v = this.vwr.ms.getAtoms(1094715393, Integer.$valueOf(this.st[i].intValue));
} else if (this.tokAt(i) == 12290 && this.tokAt(i + 1) == 2) {
v = this.vwr.ms.getAtomsFromAtomNumberInFrame(this.st[++i].intValue);
} else {
v = this.getParameter($var, 0, true);
}if (!isExpression && !isSetAt) isClauseDefine = true;
}tok = this.tokAt(0);
forceString = new Boolean (forceString | (JS.T.tokAttr(tok, 20480) || tok == 134222850)).valueOf();
if (v == null) {
fixed[j] = JS.T.tokenAll;
} else if (Clazz.instanceOf(v,"JS.SV")) {
fixed[j] = v;
} else if (Clazz.instanceOf(v, Boolean)) {
fixed[j] = ((v).booleanValue() ? JS.T.tokenOn : JS.T.tokenOff);
} else if (Clazz.instanceOf(v, Integer)) {
fixed[j] = JS.T.tv(2, (v).intValue(), v);
} else if (Clazz.instanceOf(v, Float)) {
fixed[j] = JS.T.tv(3, JU.Edge.getFloatEncodedInt("" + v), v);
} else if ((typeof(v)=='string')) {
if (!forceString && !isExpression) {
if ((tok != 36867 || j > 1 && this.st[1].tok != 537022465 && !"labelfor".equalsIgnoreCase(this.st[1].value.toString())) && JS.T.tokAttr(tok, 36864)) {
v = this.getParameter(v, 1073742190, true);
}if ((typeof(v)=='string')) {
v = this.getStringObjectAsVariable(v);
}}if (Clazz.instanceOf(v,"JS.SV")) {
fixed[j] = v;
} else {
s = v;
if (isExpression && !forceString) {
fixed[j] = (s.indexOf("|") >= 0 || JS.T.tokAttr(fixed[j - 1].tok, 268435712) ? JS.T.o(4, s) : JS.T.o(10, this.getAtomBitSet(s)));
} else {
tok = (isSetAt ? JS.T.getTokFromName(s) : isClauseDefine || forceString || s.length == 0 || s.indexOf(".") >= 0 || s.indexOf(" ") >= 0 || s.indexOf("=") >= 0 || s.indexOf(";") >= 0 || s.indexOf("[") >= 0 || s.indexOf("{") >= 0 ? 4 : 1073741824);
fixed[j] = JS.T.o(tok, v);
}}} else if (Clazz.instanceOf(v,"JU.BArray")) {
fixed[j] = JS.SV.newV(15, v);
} else if (Clazz.instanceOf(v,"JU.BS")) {
fixed[j] = JS.SV.newV(10, v);
} else if (Clazz.instanceOf(v,"JU.P3")) {
fixed[j] = JS.SV.newV(8, v);
} else if (Clazz.instanceOf(v,"JU.P4")) {
fixed[j] = JS.SV.newV(9, v);
} else if (Clazz.instanceOf(v,"JU.M34")) {
fixed[j] = JS.SV.newV(Clazz.instanceOf(v,"JU.M4") ? 12 : 11, v);
} else if (Clazz.instanceOf(v,"java.util.Map") || Clazz.instanceOf(v,"JS.ScriptContext") && (v = (v).getFullMap()) != null) {
fixed[j] = JS.SV.newV(6, (isExpression ? v : JS.SV.deepCopy(v, true, true)));
} else if (Clazz.instanceOf(v,"JU.Lst")) {
if (!isExpression) {
fixed[j] = JS.SV.newV(7, JS.SV.deepCopy(v, false, true));
break;
}var sv = v;
var bs = null;
for (var k = 0; k < sv.size(); k++) {
var svk = sv.get(k);
if (svk.tok != 10) {
bs = null;
break;
}if (bs == null) bs =  new JU.BS();
bs.or(svk.value);
}
fixed[j] = (bs == null ? JS.SV.getVariable(v) : JS.T.o(10, bs));
} else {
var center = (this).getObjectCenter($var, -2147483648, -2147483648);
if (center == null) this.invArg();
fixed[j] = JS.T.o(8, center);
}if (isSetAt && !JS.T.tokAttr(fixed[j].tok, 536870912)) this.invArg();
break;
}
j++;
}
this.st = fixed;
for (i = j; i < this.st.length; i++) this.st[i] = null;

this.slen = j;
return true;
}, "~A,~N");
Clazz.defineMethod(c$, "isFunction", 
function(sf){
return (this.getFunction(sf) != null);
}, "~S");
Clazz.defineMethod(c$, "addFunction", 
function(f){
if (f == null || f.isPrivate) {
if (this.privateFuncs == null) this.privateFuncs =  new java.util.Hashtable();
if (f != null) this.privateFuncs.put(f.name, f);
} else {
this.vwr.addFunction(f);
}}, "JS.ScriptFunction");
Clazz.defineMethod(c$, "getFunction", 
function(sf){
var f = (this.privateFuncs == null ? null : this.privateFuncs.get(sf));
return (f == null ? this.vwr.getFunction(sf) : f);
}, "~S");
});
;//5.0.1-v7 Mon Jul 28 06:27:19 CDT 2025
